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* [SPARK-3094] [PySpark] compatitable with PyPyDavies Liu2014-09-121-9/+76
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | After this patch, we can run PySpark in PyPy (testing with PyPy 2.3.1 in Mac 10.9), for example: ``` PYSPARK_PYTHON=pypy ./bin/spark-submit wordcount.py ``` The performance speed up will depend on work load (from 20% to 3000%). Here are some benchmarks: Job | CPython 2.7 | PyPy 2.3.1 | Speed up ------- | ------------ | ------------- | ------- Word Count | 41s | 15s | 2.7x Sort | 46s | 44s | 1.05x Stats | 174s | 3.6s | 48x Here is the code used for benchmark: ```python rdd = sc.textFile("text") def wordcount(): rdd.flatMap(lambda x:x.split('/'))\ .map(lambda x:(x,1)).reduceByKey(lambda x,y:x+y).collectAsMap() def sort(): rdd.sortBy(lambda x:x, 1).count() def stats(): sc.parallelize(range(1024), 20).flatMap(lambda x: xrange(5024)).stats() ``` Author: Davies Liu <davies.liu@gmail.com> Closes #2144 from davies/pypy and squashes the following commits: 9aed6c5 [Davies Liu] use protocol 2 in CloudPickle 4bc1f04 [Davies Liu] refactor b20ab3a [Davies Liu] pickle sys.stdout and stderr in portable way 3ca2351 [Davies Liu] Merge branch 'master' into pypy fae8b19 [Davies Liu] improve attrgetter, add tests 591f830 [Davies Liu] try to run tests with PyPy in run-tests c8d62ba [Davies Liu] cleanup f651fd0 [Davies Liu] fix tests using array with PyPy 1b98fb3 [Davies Liu] serialize itemgetter/attrgetter in portable ways 3c1dbfe [Davies Liu] Merge branch 'master' into pypy 42fb5fa [Davies Liu] Merge branch 'master' into pypy cb2d724 [Davies Liu] fix tests 9986692 [Davies Liu] Merge branch 'master' into pypy 25b4ca7 [Davies Liu] support PyPy
* [SPARK-3458] enable python "with" statements for SparkContextMatthew Farrellee2014-09-091-0/+29
| | | | | | | | | | | | | | | | | | | | | | | | | allow for best practice code, ``` try: sc = SparkContext() app(sc) finally: sc.stop() ``` to be written using a "with" statement, ``` with SparkContext() as sc: app(sc) ``` Author: Matthew Farrellee <matt@redhat.com> Closes #2335 from mattf/SPARK-3458 and squashes the following commits: 5b4e37c [Matthew Farrellee] [SPARK-3458] enable python "with" statements for SparkContext
* SPARK-2978. Transformation with MR shuffle semanticsSandy Ryza2014-09-081-0/+8
| | | | | | | | | | | | | | | | | | I didn't add this to the transformations list in the docs because it's kind of obscure, but would be happy to do so if others think it would be helpful. Author: Sandy Ryza <sandy@cloudera.com> Closes #2274 from sryza/sandy-spark-2978 and squashes the following commits: 4a5332a [Sandy Ryza] Fix Java test c04b447 [Sandy Ryza] Fix Python doc and add back deleted code 433ad5b [Sandy Ryza] Add Java test 4c25a54 [Sandy Ryza] Add s at the end and a couple other fixes 9b0ba99 [Sandy Ryza] Fix compilation 36e0571 [Sandy Ryza] Fix import ordering 48c12c2 [Sandy Ryza] Add Java version and additional doc e5381cd [Sandy Ryza] Fix python style warnings f147634 [Sandy Ryza] SPARK-2978. Transformation with MR shuffle semantics
* [SPARK-3415] [PySpark] removes SerializingAdapter codeWard Viaene2014-09-071-0/+11
| | | | | | | | | | | | | | | | This code removes the SerializingAdapter code that was copied from PiCloud Author: Ward Viaene <ward.viaene@bigdatapartnership.com> Closes #2287 from wardviaene/feature/pythonsys and squashes the following commits: 5f0d426 [Ward Viaene] SPARK-3415: modified test class to do dump and load 5f5d559 [Ward Viaene] SPARK-3415: modified test class name and call cloudpickle.dumps instead using StringIO afc4a9a [Ward Viaene] SPARK-3415: added newlines to pass lint aaf10b7 [Ward Viaene] SPARK-3415: removed references to SerializingAdapter and rewrote test 65ffeff [Ward Viaene] removed duplicate test a958866 [Ward Viaene] SPARK-3415: test script e263bf5 [Ward Viaene] SPARK-3415: removes legacy SerializingAdapter code
* [SPARK-2334] fix AttributeError when call PipelineRDD.id()Davies Liu2014-09-061-0/+9
| | | | | | | | | | | | | | | The underline JavaRDD for PipelineRDD is created lazily, it's delayed until call _jrdd. The id of JavaRDD is cached as `_id`, it saves a RPC call in py4j for later calls. closes #1276 Author: Davies Liu <davies.liu@gmail.com> Closes #2296 from davies/id and squashes the following commits: e197958 [Davies Liu] fix style 9721716 [Davies Liu] fix id of PipelineRDD
* [SPARK-3335] [SQL] [PySpark] support broadcast in Python UDFDavies Liu2014-09-031-0/+22
| | | | | | | | | | After this patch, broadcast can be used in Python UDF. Author: Davies Liu <davies.liu@gmail.com> Closes #2243 from davies/udf_broadcast and squashes the following commits: 7b88861 [Davies Liu] support broadcast in UDF
* [SPARK-2871] [PySpark] add countApproxDistinct() APIDavies Liu2014-09-021-0/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | RDD.countApproxDistinct(relativeSD=0.05): :: Experimental :: Return approximate number of distinct elements in the RDD. The algorithm used is based on streamlib's implementation of "HyperLogLog in Practice: Algorithmic Engineering of a State of The Art Cardinality Estimation Algorithm", available <a href="http://dx.doi.org/10.1145/2452376.2452456">here</a>. This support all the types of objects, which is supported by Pyrolite, nearly all builtin types. param relativeSD Relative accuracy. Smaller values create counters that require more space. It must be greater than 0.000017. >>> n = sc.parallelize(range(1000)).map(str).countApproxDistinct() >>> 950 < n < 1050 True >>> n = sc.parallelize([i % 20 for i in range(1000)]).countApproxDistinct() >>> 18 < n < 22 True Author: Davies Liu <davies.liu@gmail.com> Closes #2142 from davies/countApproxDistinct and squashes the following commits: e20da47 [Davies Liu] remove the correction in Python c38c4e4 [Davies Liu] fix doc tests 2ab157c [Davies Liu] fix doc tests 9d2565f [Davies Liu] add commments and link for hash collision correction d306492 [Davies Liu] change range of hash of tuple to [0, maxint] ded624f [Davies Liu] calculate hash in Python 4cba98f [Davies Liu] add more tests a85a8c6 [Davies Liu] Merge branch 'master' into countApproxDistinct e97e342 [Davies Liu] add countApproxDistinct()
* [SPARK-3073] [PySpark] use external sort in sortBy() and sortByKey()Davies Liu2014-08-261-1/+41
| | | | | | | | | | | | | | | | | Using external sort to support sort large datasets in reduce stage. Author: Davies Liu <davies.liu@gmail.com> Closes #1978 from davies/sort and squashes the following commits: bbcd9ba [Davies Liu] check spilled bytes in tests b125d2f [Davies Liu] add test for external sort in rdd eae0176 [Davies Liu] choose different disks from different processes and instances 1f075ed [Davies Liu] Merge branch 'master' into sort eb53ca6 [Davies Liu] Merge branch 'master' into sort 644abaf [Davies Liu] add license in LICENSE 19f7873 [Davies Liu] improve tests 55602ee [Davies Liu] use external sort in sortBy() and sortByKey()
* [SPARK-2871] [PySpark] add histgram() APIDavies Liu2014-08-261-0/+104
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | RDD.histogram(buckets) Compute a histogram using the provided buckets. The buckets are all open to the right except for the last which is closed. e.g. [1,10,20,50] means the buckets are [1,10) [10,20) [20,50], which means 1<=x<10, 10<=x<20, 20<=x<=50. And on the input of 1 and 50 we would have a histogram of 1,0,1. If your histogram is evenly spaced (e.g. [0, 10, 20, 30]), this can be switched from an O(log n) inseration to O(1) per element(where n = # buckets). Buckets must be sorted and not contain any duplicates, must be at least two elements. If `buckets` is a number, it will generates buckets which is evenly spaced between the minimum and maximum of the RDD. For example, if the min value is 0 and the max is 100, given buckets as 2, the resulting buckets will be [0,50) [50,100]. buckets must be at least 1 If the RDD contains infinity, NaN throws an exception If the elements in RDD do not vary (max == min) always returns a single bucket. It will return an tuple of buckets and histogram. >>> rdd = sc.parallelize(range(51)) >>> rdd.histogram(2) ([0, 25, 50], [25, 26]) >>> rdd.histogram([0, 5, 25, 50]) ([0, 5, 25, 50], [5, 20, 26]) >>> rdd.histogram([0, 15, 30, 45, 60], True) ([0, 15, 30, 45, 60], [15, 15, 15, 6]) >>> rdd = sc.parallelize(["ab", "ac", "b", "bd", "ef"]) >>> rdd.histogram(("a", "b", "c")) (('a', 'b', 'c'), [2, 2]) closes #122, it's duplicated. Author: Davies Liu <davies.liu@gmail.com> Closes #2091 from davies/histgram and squashes the following commits: a322f8a [Davies Liu] fix deprecation of e.message 84e85fa [Davies Liu] remove evenBuckets, add more tests (including str) d9a0722 [Davies Liu] address comments 0e18a2d [Davies Liu] add histgram() API
* [SPARK-2790] [PySpark] fix zip with serializers which have different batch ↵Davies Liu2014-08-191-1/+26
| | | | | | | | | | | | | | | sizes. If two RDDs have different batch size in serializers, then it will try to re-serialize the one with smaller batch size, then call RDD.zip() in Spark. Author: Davies Liu <davies.liu@gmail.com> Closes #1894 from davies/zip and squashes the following commits: c4652ea [Davies Liu] add more test cases 6d05fc8 [Davies Liu] Merge branch 'master' into zip 813b1e4 [Davies Liu] add more tests for failed cases a4aafda [Davies Liu] fix zip with serializers which have different batch sizes.
* [SPARK-3103] [PySpark] fix saveAsTextFile() with utf-8Davies Liu2014-08-181-0/+9
| | | | | | | | | | bugfix: It will raise an exception when it try to encode non-ASCII strings into unicode. It should only encode unicode as "utf-8". Author: Davies Liu <davies.liu@gmail.com> Closes #2018 from davies/fix_utf8 and squashes the following commits: 4db7967 [Davies Liu] fix saveAsTextFile() with utf-8
* [SPARK-1065] [PySpark] improve supporting for large broadcastDavies Liu2014-08-161-0/+7
| | | | | | | | | | | | | | | | | | Passing large object by py4j is very slow (cost much memory), so pass broadcast objects via files (similar to parallelize()). Add an option to keep object in driver (it's False by default) to save memory in driver. Author: Davies Liu <davies.liu@gmail.com> Closes #1912 from davies/broadcast and squashes the following commits: e06df4a [Davies Liu] load broadcast from disk in driver automatically db3f232 [Davies Liu] fix serialization of accumulator 631a827 [Davies Liu] Merge branch 'master' into broadcast c7baa8c [Davies Liu] compress serrialized broadcast and command 9a7161f [Davies Liu] fix doc tests e93cf4b [Davies Liu] address comments: add test 6226189 [Davies Liu] improve large broadcast
* [PySpark] [SPARK-2954] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 FixesJosh Rosen2014-08-111-3/+10
| | | | | | | | | | | | | | | | | - Modify python/run-tests to test with Python 2.6 - Use unittest2 when running on Python 2.6. - Fix issue with namedtuple. - Skip TestOutputFormat.test_newhadoop on Python 2.6 until SPARK-2951 is fixed. - Fix MLlib _deserialize_double on Python 2.6. Closes #1868. Closes #1042. Author: Josh Rosen <joshrosen@apache.org> Closes #1874 from JoshRosen/python2.6 and squashes the following commits: 983d259 [Josh Rosen] [SPARK-2954] Fix MLlib _deserialize_double on Python 2.6. 5d18fd7 [Josh Rosen] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 fixes
* [SPARK-2627] [PySpark] have the build enforce PEP 8 automaticallyNicholas Chammas2014-08-061-62/+81
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | As described in [SPARK-2627](https://issues.apache.org/jira/browse/SPARK-2627), we'd like Python code to automatically be checked for PEP 8 compliance by Jenkins. This pull request aims to do that. Notes: * We may need to install [`pep8`](https://pypi.python.org/pypi/pep8) on the build server. * I'm expecting tests to fail now that PEP 8 compliance is being checked as part of the build. I'm fine with cleaning up any remaining PEP 8 violations as part of this pull request. * I did not understand why the RAT and scalastyle reports are saved to text files. I did the same for the PEP 8 check, but only so that the console output style can match those for the RAT and scalastyle checks. The PEP 8 report is removed right after the check is complete. * Updates to the ["Contributing to Spark"](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) guide will be submitted elsewhere, as I don't believe that text is part of the Spark repo. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Author: nchammas <nicholas.chammas@gmail.com> Closes #1744 from nchammas/master and squashes the following commits: 274b238 [Nicholas Chammas] [SPARK-2627] [PySpark] minor indentation changes 983d963 [nchammas] Merge pull request #5 from apache/master 1db5314 [nchammas] Merge pull request #4 from apache/master 0e0245f [Nicholas Chammas] [SPARK-2627] undo erroneous whitespace fixes bf30942 [Nicholas Chammas] [SPARK-2627] PEP8: comment spacing 6db9a44 [nchammas] Merge pull request #3 from apache/master 7b4750e [Nicholas Chammas] merge upstream changes 91b7584 [Nicholas Chammas] [SPARK-2627] undo unnecessary line breaks 44e3e56 [Nicholas Chammas] [SPARK-2627] use tox.ini to exclude files b09fae2 [Nicholas Chammas] don't wrap comments unnecessarily bfb9f9f [Nicholas Chammas] [SPARK-2627] keep up with the PEP 8 fixes 9da347f [nchammas] Merge pull request #2 from apache/master aa5b4b5 [Nicholas Chammas] [SPARK-2627] follow Spark bash style for if blocks d0a83b9 [Nicholas Chammas] [SPARK-2627] check that pep8 downloaded fine dffb5dd [Nicholas Chammas] [SPARK-2627] download pep8 at runtime a1ce7ae [Nicholas Chammas] [SPARK-2627] space out test report sections 21da538 [Nicholas Chammas] [SPARK-2627] it's PEP 8, not PEP8 6f4900b [Nicholas Chammas] [SPARK-2627] more misc PEP 8 fixes fe57ed0 [Nicholas Chammas] removing merge conflict backups 9c01d4c [nchammas] Merge pull request #1 from apache/master 9a66cb0 [Nicholas Chammas] resolving merge conflicts a31ccc4 [Nicholas Chammas] [SPARK-2627] miscellaneous PEP 8 fixes beaa9ac [Nicholas Chammas] [SPARK-2627] fail check on non-zero status 723ed39 [Nicholas Chammas] always delete the report file 0541ebb [Nicholas Chammas] [SPARK-2627] call Python linter from run-tests 12440fa [Nicholas Chammas] [SPARK-2627] add Scala linter 61c07b9 [Nicholas Chammas] [SPARK-2627] add Python linter 75ad552 [Nicholas Chammas] make check output style consistent
* [SPARK-1687] [PySpark] pickable namedtupleDavies Liu2014-08-041-0/+19
| | | | | | | | | | | | | | | | | | | | Add an hook to replace original namedtuple with an pickable one, then namedtuple could be used in RDDs. PS: pyspark should be import BEFORE "from collections import namedtuple" Author: Davies Liu <davies.liu@gmail.com> Closes #1623 from davies/namedtuple and squashes the following commits: 045dad8 [Davies Liu] remove unrelated code changes 4132f32 [Davies Liu] address comment 55b1c1a [Davies Liu] fix tests 61f86eb [Davies Liu] replace all the reference of namedtuple to new hacked one 98df6c6 [Davies Liu] Merge branch 'master' of github.com:apache/spark into namedtuple f7b1bde [Davies Liu] add hack for CloudPickleSerializer 0c5c849 [Davies Liu] Merge branch 'master' of github.com:apache/spark into namedtuple 21991e6 [Davies Liu] hack namedtuple in __main__ module, make it picklable. 93b03b8 [Davies Liu] pickable namedtuple
* [SPARK-1740] [PySpark] kill the python workerDavies Liu2014-08-031-0/+51
| | | | | | | | | | | | | | | | Kill only the python worker related to cancelled tasks. The daemon will start a background thread to monitor all the opened sockets for all workers. If the socket is closed by JVM, this thread will kill the worker. When an task is cancelled, the socket to worker will be closed, then the worker will be killed by deamon. Author: Davies Liu <davies.liu@gmail.com> Closes #1643 from davies/kill and squashes the following commits: 8ffe9f3 [Davies Liu] kill worker by deamon, because runtime.exec() is too heavy 46ca150 [Davies Liu] address comment acd751c [Davies Liu] kill the worker when task is canceled
* StatCounter on NumPy arrays [PYSPARK][SPARK-2012]Jeremy Freeman2014-08-011-0/+24
| | | | | | | | | | | | | | | | | | | These changes allow StatCounters to work properly on NumPy arrays, to fix the issue reported here (https://issues.apache.org/jira/browse/SPARK-2012). If NumPy is installed, the NumPy functions ``maximum``, ``minimum``, and ``sqrt``, which work on arrays, are used to merge statistics. If not, we fall back on scalar operators, so it will work on arrays with NumPy, but will also work without NumPy. New unit tests added, along with a check for NumPy in the tests. Author: Jeremy Freeman <the.freeman.lab@gmail.com> Closes #1725 from freeman-lab/numpy-max-statcounter and squashes the following commits: fe973b1 [Jeremy Freeman] Avoid duplicate array import in tests 7f0e397 [Jeremy Freeman] Refactored check for numpy 8e764dd [Jeremy Freeman] Explicit numpy imports 875414c [Jeremy Freeman] Fixed indents 1c8a832 [Jeremy Freeman] Unit tests for StatCounter with NumPy arrays 176a127 [Jeremy Freeman] Use numpy arrays in StatCounter
* [SPARK-2024] Add saveAsSequenceFile to PySparkKan Zhang2014-07-301-13/+304
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | JIRA issue: https://issues.apache.org/jira/browse/SPARK-2024 This PR is a followup to #455 and adds capabilities for saving PySpark RDDs using SequenceFile or any Hadoop OutputFormats. * Added RDD methods ```saveAsSequenceFile```, ```saveAsHadoopFile``` and ```saveAsHadoopDataset```, for both old and new MapReduce APIs. * Default converter for converting common data types to Writables. Users may specify custom converters to convert to desired data types. * No out-of-box support for reading/writing arrays, since ArrayWritable itself doesn't have a no-arg constructor for creating an empty instance upon reading. Users need to provide ArrayWritable subtypes. Custom converters for converting arrays to suitable ArrayWritable subtypes are also needed when writing. When reading, the default converter will convert any custom ArrayWritable subtypes to ```Object[]``` and they get pickled to Python tuples. * Added HBase and Cassandra output examples to show how custom output formats and converters can be used. cc MLnick mateiz ahirreddy pwendell Author: Kan Zhang <kzhang@apache.org> Closes #1338 from kanzhang/SPARK-2024 and squashes the following commits: c01e3ef [Kan Zhang] [SPARK-2024] code formatting 6591e37 [Kan Zhang] [SPARK-2024] renaming pickled -> pickledRDD d998ad6 [Kan Zhang] [SPARK-2024] refectoring to get method params below 10 57a7a5e [Kan Zhang] [SPARK-2024] correcting typo 75ca5bd [Kan Zhang] [SPARK-2024] Better type checking for batch serialized RDD 0bdec55 [Kan Zhang] [SPARK-2024] Refactoring newly added tests 9f39ff4 [Kan Zhang] [SPARK-2024] Adding 2 saveAsHadoopDataset tests 0c134f3 [Kan Zhang] [SPARK-2024] Test refactoring and adding couple unbatched cases 7a176df [Kan Zhang] [SPARK-2024] Add saveAsSequenceFile to PySpark
* [SPARK-791] [PySpark] fix pickle itemgetter with cloudpickleDavies Liu2014-07-291-0/+6
| | | | | | | | | | fix the problem with pickle operator.itemgetter with multiple index. Author: Davies Liu <davies.liu@gmail.com> Closes #1627 from davies/itemgetter and squashes the following commits: aabd7fa [Davies Liu] fix pickle itemgetter with cloudpickle
* [SPARK-2580] [PySpark] keep silent in worker if JVM close the socketDavies Liu2014-07-291-0/+6
| | | | | | | | | | | | | During rdd.take(n), JVM will close the socket if it had got enough data, the Python worker should keep silent in this case. In the same time, the worker should not print the trackback into stderr if it send the traceback to JVM successfully. Author: Davies Liu <davies.liu@gmail.com> Closes #1625 from davies/error and squashes the following commits: 4fbcc6d [Davies Liu] disable log4j during testing when exception is expected. cc14202 [Davies Liu] keep silent in worker if JVM close the socket
* [SPARK-1550] [PySpark] Allow SparkContext creation after failed attemptsJosh Rosen2014-07-271-0/+6
| | | | | | | | | | This addresses a PySpark issue where a failed attempt to construct SparkContext would prevent any future SparkContext creation. Author: Josh Rosen <joshrosen@apache.org> Closes #1606 from JoshRosen/SPARK-1550 and squashes the following commits: ec7fadc [Josh Rosen] [SPARK-1550] [PySpark] Allow SparkContext creation after failed attempts
* [SPARK-2601] [PySpark] Fix Py4J error when transforming pickleFilesJosh Rosen2014-07-261-0/+9
| | | | | | | | | | Similar to SPARK-1034, the problem was that Py4J didn’t cope well with the fake ClassTags used in the Java API. It doesn’t look like there’s any reason why PythonRDD needs to take a ClassTag, since it just ignores the type of the previous RDD, so I removed the type parameter and we no longer pass ClassTags from Python. Author: Josh Rosen <joshrosen@apache.org> Closes #1605 from JoshRosen/spark-2601 and squashes the following commits: b68e118 [Josh Rosen] Fix Py4J error when transforming pickleFiles [SPARK-2601]
* [SPARK-2538] [PySpark] Hash based disk spilling aggregationDavies Liu2014-07-241-0/+57
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | During aggregation in Python worker, if the memory usage is above spark.executor.memory, it will do disk spilling aggregation. It will split the aggregation into multiple stage, in each stage, it will partition the aggregated data by hash and dump them into disks. After all the data are aggregated, it will merge all the stages together (partition by partition). Author: Davies Liu <davies.liu@gmail.com> Closes #1460 from davies/spill and squashes the following commits: cad91bf [Davies Liu] call gc.collect() after data.clear() to release memory as much as possible. 37d71f7 [Davies Liu] balance the partitions 902f036 [Davies Liu] add shuffle.py into run-tests dcf03a9 [Davies Liu] fix memory_info() of psutil 67e6eba [Davies Liu] comment for MAX_TOTAL_PARTITIONS f6bd5d6 [Davies Liu] rollback next_limit() again, the performance difference is huge: e74b785 [Davies Liu] fix code style and change next_limit to memory_limit 400be01 [Davies Liu] address all the comments 6178844 [Davies Liu] refactor and improve docs fdd0a49 [Davies Liu] add long doc string for ExternalMerger 1a97ce4 [Davies Liu] limit used memory and size of objects in partitionBy() e6cc7f9 [Davies Liu] Merge branch 'master' into spill 3652583 [Davies Liu] address comments e78a0a0 [Davies Liu] fix style 24cec6a [Davies Liu] get local directory by SPARK_LOCAL_DIR 57ee7ef [Davies Liu] update docs 286aaff [Davies Liu] let spilled aggregation in Python configurable e9a40f6 [Davies Liu] recursive merger 6edbd1f [Davies Liu] Hash based disk spilling aggregation
* [SPARK-2470] PEP8 fixes to PySparkNicholas Chammas2014-07-211-3/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This pull request aims to resolve all outstanding PEP8 violations in PySpark. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Author: nchammas <nicholas.chammas@gmail.com> Closes #1505 from nchammas/master and squashes the following commits: 98171af [Nicholas Chammas] [SPARK-2470] revert PEP 8 fixes to cloudpickle cba7768 [Nicholas Chammas] [SPARK-2470] wrap expression list in parentheses e178dbe [Nicholas Chammas] [SPARK-2470] style - change position of line break 9127d2b [Nicholas Chammas] [SPARK-2470] wrap expression lists in parentheses 22132a4 [Nicholas Chammas] [SPARK-2470] wrap conditionals in parentheses 24639bc [Nicholas Chammas] [SPARK-2470] fix whitespace for doctest 7d557b7 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to tests.py 8f8e4c0 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to storagelevel.py b3b96cf [Nicholas Chammas] [SPARK-2470] PEP8 fixes to statcounter.py d644477 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to worker.py aa3a7b6 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to sql.py 1916859 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to shell.py 95d1d95 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to serializers.py a0fec2e [Nicholas Chammas] [SPARK-2470] PEP8 fixes to mllib c85e1e5 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to join.py d14f2f1 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to __init__.py 81fcb20 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to resultiterable.py 1bde265 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to java_gateway.py 7fc849c [Nicholas Chammas] [SPARK-2470] PEP8 fixes to daemon.py ca2d28b [Nicholas Chammas] [SPARK-2470] PEP8 fixes to context.py f4e0039 [Nicholas Chammas] [SPARK-2470] PEP8 fixes to conf.py a6d5e4b [Nicholas Chammas] [SPARK-2470] PEP8 fixes to cloudpickle.py f0a7ebf [Nicholas Chammas] [SPARK-2470] PEP8 fixes to rddsampler.py 4dd148f [nchammas] Merge pull request #5 from apache/master f7e4581 [Nicholas Chammas] unrelated pep8 fix a36eed0 [Nicholas Chammas] name ec2 instances and security groups consistently de7292a [nchammas] Merge pull request #4 from apache/master 2e4fe00 [nchammas] Merge pull request #3 from apache/master 89fde08 [nchammas] Merge pull request #2 from apache/master 69f6e22 [Nicholas Chammas] PEP8 fixes 2627247 [Nicholas Chammas] broke up lines before they hit 100 chars 6544b7e [Nicholas Chammas] [SPARK-2065] give launched instances names 69da6cf [nchammas] Merge pull request #1 from apache/master
* SPARK-554. Add aggregateByKey.Sandy Ryza2014-06-121-0/+15
| | | | | | | | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #705 from sryza/sandy-spark-554 and squashes the following commits: 2302b8f [Sandy Ryza] Add MIMA exclude f52e0ad [Sandy Ryza] Fix Python tests for real 2f3afa3 [Sandy Ryza] Fix Python test 0b735e9 [Sandy Ryza] Fix line lengths ae56746 [Sandy Ryza] Fix doc (replace T with V) c2be415 [Sandy Ryza] Java and Python aggregateByKey 23bf400 [Sandy Ryza] SPARK-554. Add aggregateByKey.
* SPARK-1416: PySpark support for SequenceFile and Hadoop InputFormatsNick Pentreath2014-06-091-0/+145
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | So I finally resurrected this PR. It seems the old one against the incubator mirror is no longer available, so I cannot reference it. This adds initial support for reading Hadoop ```SequenceFile```s, as well as arbitrary Hadoop ```InputFormat```s, in PySpark. # Overview The basics are as follows: 1. ```PythonRDD``` object contains the relevant methods, that are in turn invoked by ```SparkContext``` in PySpark 2. The SequenceFile or InputFormat is read on the Scala side and converted from ```Writable``` instances to the relevant Scala classes (in the case of primitives) 3. Pyrolite is used to serialize Java objects. If this fails, the fallback is ```toString``` 4. ```PickleSerializer``` on the Python side deserializes. This works "out the box" for simple ```Writable```s: * ```Text``` * ```IntWritable```, ```DoubleWritable```, ```FloatWritable``` * ```NullWritable``` * ```BooleanWritable``` * ```BytesWritable``` * ```MapWritable``` It also works for simple, "struct-like" classes. Due to the way Pyrolite works, this requires that the classes satisfy the JavaBeans convenstions (i.e. with fields and a no-arg constructor and getters/setters). (Perhaps in future some sugar for case classes and reflection could be added). I've tested it out with ```ESInputFormat``` as an example and it works very nicely: ```python conf = {"es.resource" : "index/type" } rdd = sc.newAPIHadoopRDD("org.elasticsearch.hadoop.mr.EsInputFormat", "org.apache.hadoop.io.NullWritable", "org.elasticsearch.hadoop.mr.LinkedMapWritable", conf=conf) rdd.first() ``` I suspect for things like HBase/Cassandra it will be a bit trickier to get it to work out the box. # Some things still outstanding: 1. ~~Requires ```msgpack-python``` and will fail without it. As originally discussed with Josh, add a ```as_strings``` argument that defaults to ```False```, that can be used if ```msgpack-python``` is not available~~ 2. ~~I see from https://github.com/apache/spark/pull/363 that Pyrolite is being used there for SerDe between Scala and Python. @ahirreddy @mateiz what is the plan behind this - is Pyrolite preferred? It seems from a cursory glance that adapting the ```msgpack```-based SerDe here to use Pyrolite wouldn't be too hard~~ 3. ~~Support the key and value "wrapper" that would allow a Scala/Java function to be plugged in that would transform whatever the key/value Writable class is into something that can be serialized (e.g. convert some custom Writable to a JavaBean or ```java.util.Map``` that can be easily serialized)~~ 4. Support ```saveAsSequenceFile``` and ```saveAsHadoopFile``` etc. This would require SerDe in the reverse direction, that can be handled by Pyrolite. Will work on this as a separate PR Author: Nick Pentreath <nick.pentreath@gmail.com> Closes #455 from MLnick/pyspark-inputformats and squashes the following commits: 268df7e [Nick Pentreath] Documentation changes mer @pwendell comments 761269b [Nick Pentreath] Address @pwendell comments, simplify default writable conversions and remove registry. 4c972d8 [Nick Pentreath] Add license headers d150431 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats cde6af9 [Nick Pentreath] Parameterize converter trait 5ebacfa [Nick Pentreath] Update docs for PySpark input formats a985492 [Nick Pentreath] Move Converter examples to own package 365d0be [Nick Pentreath] Make classes private[python]. Add docs and @Experimental annotation to Converter interface. eeb8205 [Nick Pentreath] Fix path relative to SPARK_HOME in tests 1eaa08b [Nick Pentreath] HBase -> Cassandra app name oversight 3f90c3e [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 2c18513 [Nick Pentreath] Add examples for reading HBase and Cassandra InputFormats from Python b65606f [Nick Pentreath] Add converter interface 5757f6e [Nick Pentreath] Default key/value classes for sequenceFile asre None 085b55f [Nick Pentreath] Move input format tests to tests.py and clean up docs 43eb728 [Nick Pentreath] PySpark InputFormats docs into programming guide 94beedc [Nick Pentreath] Clean up args in PythonRDD. Set key/value converter defaults to None for PySpark context.py methods 1a4a1d6 [Nick Pentreath] Address @mateiz style comments 01e0813 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 15a7d07 [Nick Pentreath] Remove default args for key/value classes. Arg names to camelCase 9fe6bd5 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 84fe8e3 [Nick Pentreath] Python programming guide space formatting d0f52b6 [Nick Pentreath] Python programming guide 7caa73a [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 93ef995 [Nick Pentreath] Add back context.py changes 9ef1896 [Nick Pentreath] Recover earlier changes lost in previous merge for serializers.py 077ecb2 [Nick Pentreath] Recover earlier changes lost in previous merge for context.py 5af4770 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 35b8e3a [Nick Pentreath] Another fix for test ordering bef3afb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats e001b94 [Nick Pentreath] Fix test failures due to ordering 78978d9 [Nick Pentreath] Add doc for SequenceFile and InputFormat support to Python programming guide 64eb051 [Nick Pentreath] Scalastyle fix e7552fa [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 44f2857 [Nick Pentreath] Remove msgpack dependency and switch serialization to Pyrolite, plus some clean up and refactoring c0ebfb6 [Nick Pentreath] Change sequencefile test data generator to easily be called from PySpark tests 1d7c17c [Nick Pentreath] Amend tests to auto-generate sequencefile data in temp dir 17a656b [Nick Pentreath] remove binary sequencefile for tests f60959e [Nick Pentreath] Remove msgpack dependency and serializer from PySpark 450e0a2 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 31a2fff [Nick Pentreath] Scalastyle fixes fc5099e [Nick Pentreath] Add Apache license headers 4e08983 [Nick Pentreath] Clean up docs for PySpark context methods b20ec7e [Nick Pentreath] Clean up merge duplicate dependencies 951c117 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats f6aac55 [Nick Pentreath] Bring back msgpack 9d2256e [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 1bbbfb0 [Nick Pentreath] Clean up SparkBuild from merge a67dfad [Nick Pentreath] Clean up Msgpack serialization and registering 7237263 [Nick Pentreath] Add back msgpack serializer and hadoop file code lost during merging 25da1ca [Nick Pentreath] Add generator for nulls, bools, bytes and maps 65360d5 [Nick Pentreath] Adding test SequenceFiles 0c612e5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats d72bf18 [Nick Pentreath] msgpack dd57922 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats e67212a [Nick Pentreath] Add back msgpack dependency f2d76a0 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 41856a5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats 97ef708 [Nick Pentreath] Remove old writeToStream 2beeedb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 795a763 [Nick Pentreath] Change name to WriteInputFormatTestDataGenerator. Cleanup some var names. Use SPARK_HOME in path for writing test sequencefile data. 174f520 [Nick Pentreath] Add back graphx settings 703ee65 [Nick Pentreath] Add back msgpack 619c0fa [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats 1c8efbc [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats eb40036 [Nick Pentreath] Remove unused comment lines 4d7ef2e [Nick Pentreath] Fix indentation f1d73e3 [Nick Pentreath] mergeConfs returns a copy rather than mutating one of the input arguments 0f5cd84 [Nick Pentreath] Remove unused pair UTF8 class. Add comments to msgpack deserializer 4294cbb [Nick Pentreath] Add old Hadoop api methods. Clean up and expand comments. Clean up argument names 818a1e6 [Nick Pentreath] Add seqencefile and Hadoop InputFormat support to PythonRDD 4e7c9e3 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats c304cc8 [Nick Pentreath] Adding supporting sequncefiles for tests. Cleaning up 4b0a43f [Nick Pentreath] Refactoring utils into own objects. Cleaning up old commented-out code d86325f [Nick Pentreath] Initial WIP of PySpark support for SequenceFile and arbitrary Hadoop InputFormat
* [SPARK-1942] Stop clearing spark.driver.port in unit testsSyed Hashmi2014-06-031-4/+0
| | | | | | | | | | | | | | | | | | | stop resetting spark.driver.port in unit tests (scala, java and python). Author: Syed Hashmi <shashmi@cloudera.com> Author: CodingCat <zhunansjtu@gmail.com> Closes #943 from syedhashmi/master and squashes the following commits: 885f210 [Syed Hashmi] Removing unnecessary file (created by mergetool) b8bd4b5 [Syed Hashmi] Merge remote-tracking branch 'upstream/master' b895e59 [Syed Hashmi] Revert "[SPARK-1784] Add a new partitioner" 57b6587 [Syed Hashmi] Revert "[SPARK-1784] Add a balanced partitioner" 1574769 [Syed Hashmi] [SPARK-1942] Stop clearing spark.driver.port in unit tests 4354836 [Syed Hashmi] Revert "SPARK-1686: keep schedule() calling in the main thread" fd36542 [Syed Hashmi] [SPARK-1784] Add a balanced partitioner 6668015 [CodingCat] SPARK-1686: keep schedule() calling in the main thread 4ca94cc [Syed Hashmi] [SPARK-1784] Add a new partitioner
* SPARK-1917: fix PySpark import of scipy.special functionsUri Laserson2014-05-311-0/+24
| | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1917 Author: Uri Laserson <laserson@cloudera.com> Closes #866 from laserson/SPARK-1917 and squashes the following commits: d947e8c [Uri Laserson] Added test for scipy.special importing 1798bbd [Uri Laserson] SPARK-1917: fix PySpark import of scipy.special
* [SPARK-1549] Add Python support to spark-submitMatei Zaharia2014-05-061-4/+127
| | | | | | | | | | | | | | | | | | | | | | This PR updates spark-submit to allow submitting Python scripts (currently only with deploy-mode=client, but that's all that was supported before) and updates the PySpark code to properly find various paths, etc. One significant change is that we assume we can always find the Python files either from the Spark assembly JAR (which will happen with the Maven assembly build in make-distribution.sh) or from SPARK_HOME (which will exist in local mode even if you use sbt assembly, and should be enough for testing). This means we no longer need a weird hack to modify the environment for YARN. This patch also updates the Python worker manager to run python with -u, which means unbuffered output (send it to our logs right away instead of waiting a while after stuff was written); this should simplify debugging. In addition, it fixes https://issues.apache.org/jira/browse/SPARK-1709, setting the main class from a JAR's Main-Class attribute if not specified by the user, and fixes a few help strings and style issues in spark-submit. In the future we may want to make the `pyspark` shell use spark-submit as well, but it seems unnecessary for 1.0. Author: Matei Zaharia <matei@databricks.com> Closes #664 from mateiz/py-submit and squashes the following commits: 15e9669 [Matei Zaharia] Fix some uses of path.separator property 051278c [Matei Zaharia] Small style fixes 0afe886 [Matei Zaharia] Add license headers 4650412 [Matei Zaharia] Add pyFiles to PYTHONPATH in executors, remove old YARN stuff, add tests 15f8e1e [Matei Zaharia] Set PYTHONPATH in PythonWorkerFactory in case it wasn't set from outside 47c0655 [Matei Zaharia] More work to make spark-submit work with Python: d4375bd [Matei Zaharia] Clean up description of spark-submit args a bit and add Python ones
* SPARK-1004. PySpark on YARNSandy Ryza2014-04-291-1/+3
| | | | | | | | | | | | This reopens https://github.com/apache/incubator-spark/pull/640 against the new repo Author: Sandy Ryza <sandy@cloudera.com> Closes #30 from sryza/sandy-spark-1004 and squashes the following commits: 89889d4 [Sandy Ryza] Move unzipping py4j to the generate-resources phase so that it gets included in the jar the first time 5165a02 [Sandy Ryza] Fix docs fd0df79 [Sandy Ryza] PySpark on YARN
* Fix for SPARK-1025: PySpark hang on missing files.Josh Rosen2014-01-231-0/+11
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* Fix SPARK-978: ClassCastException in PySpark cartesian.Josh Rosen2014-01-231-0/+9
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* Fix SPARK-1034: Py4JException on PySpark Cartesian ResultJosh Rosen2014-01-231-0/+7
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* Fixed Python API for sc.setCheckpointDir. Also other fixes based on ↵Tathagata Das2013-12-241-2/+2
| | | | Reynold's comments on PR 289.
* Fix UnicodeEncodeError in PySpark saveAsTextFile().Josh Rosen2013-11-281-0/+15
| | | Fixes SPARK-970.
* Add custom serializer support to PySpark.Josh Rosen2013-11-101-1/+2
| | | | | | | | | For now, this only adds MarshalSerializer, but it lays the groundwork for other supporting custom serializers. Many of these mechanisms can also be used to support deserialization of different data formats sent by Java, such as data encoded by MsgPack. This also fixes a bug in SparkContext.union().
* Implementing SPARK-878 for PySpark: adding zip and egg files to context and ↵Andre Schumacher2013-08-161-0/+11
| | | | passing it down to workers which add these to their sys.path
* Fix PySpark unit tests on Python 2.6.Josh Rosen2013-08-141-5/+8
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* Add Apache license headers and LICENSE and NOTICE filesMatei Zaharia2013-07-161-0/+17
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* Add tests and fixes for Python daemon shutdownJey Kottalam2013-06-211-0/+43
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* Do not launch JavaGateways on workers (SPARK-674).Josh Rosen2013-02-011-1/+1
| | | | | | | | | | | The problem was that the gateway was being initialized whenever the pyspark.context module was loaded. The fix uses lazy initialization that occurs only when SparkContext instances are actually constructed. I also made the gateway and jvm variables private. This change results in ~3-4x performance improvement when running the PySpark unit tests.
* Fix stdout redirection in PySpark.Josh Rosen2013-02-011-0/+9
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* Replace old 'master' term with 'driver'.Stephen Haberman2013-01-251-1/+1
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* Allow PySpark's SparkFiles to be used from driverJosh Rosen2013-01-231-0/+23
| | | | Fix minor documentation formatting issues.
* Fix sys.path bug in PySpark SparkContext.addPyFileJosh Rosen2013-01-221-5/+33
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* Clean up setup code in PySpark checkpointing testsJosh Rosen2013-01-201-14/+5
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* Add checkpointFile() and more tests to PySpark.Josh Rosen2013-01-201-0/+24
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* Add RDD checkpointing to Python API.Josh Rosen2013-01-201-0/+46
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